Synthetic Genomics - the Sci-Fi and the Promise

Synthetic Genomics, an R&D think-tank, is opening a $600 million R&D Center with Exxon. This is shocking because Exxon has been hard-core in ignoring alternative energy. Synthetic Genomics has already lined up financing with BP. What has attracted biofuel opponent Exxon to an odd-ball technology like algae biofuel?

I, myself, have criticized algae energy as a fantasy. (This post has economics per acre of different biofuel crops.)

Synthetic Genomics' name comes from founder Craig Venter's science fiction idea of stitching together genes & other cellular structures to make "artificial organisms" as little biochemical factories, according to geneticist Paul Arnold. They have the patent on synthetic organism.

This reminds me of science fiction movies, like Blade Runner. Scary or not this technology could be pretty cool.

This is the same Craig Venter whose "shotgun" sequencing technology grabbed patents at the end of the human genome project.

Hard-boiled Exxon would never buy into Sci-Fi fantasy. The real JV is much more modest. It has a pretty straight forward six step plan. Synthetic Genomics will be developing an algae strain optimized for lipid (oil) production. They will separate the algae, and then make biodiesel from it.

Algae biofuel is not new. Wikipedia has an extensive entry, and this site has fifteen algae energy start-ups.

It seems that power hitters like Exxon, BP and Bill Gate through Sapphire Energy, and sinking money into this. There must be a clever technology that is making this economical. I could not find any Synthetic Genomics patents that would describe it. Maybe they are under another assignee.

(The guys in the photo of algae bioreactors are Kertz & Frater, who develop such equipment.)

See my follow-up posting on synthetic biology.

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Dow Invests in Algae too! Why All the Money Flowing to Algae Biofuel??

C&E News reports that Dow has joined the biofuel algae fad. This makes two giant multinationals to plunk down money on biofuel from algae in the last month. [See my previous post on Exxon & BP's investment in Synthetic Genomics.]

Dow and Algenol is building a plant next to Dow's giant chemical complex in Freeport, Texas. Algenols technology is interesting because if makes ethanol directly. It would be particularly interesting if the cells excrete the ethanol, so they don't have to be killed.

Note that the Algenol plants has open tanks. These are easier to build, but previous algae plants have had trouble keeping the algae healthy because of rainwater and evaporation.

Why are big oil and chemical companies buying into algae?

1. Algae plants are big consumers of CO2, carbon dioxide. This could be a cheap way to get carbon dioxide credits in some future greenhouse gas tariff system.

2. Algenol's technology generates ethanol directly, and Synthetic Genomic's technology generates biodiesel. This is much better than other biofuels that need extensive processing. For example corn needs to be fermented to make ethanol.

3. Blogger Christopher Haase says algae plants also transform salt water into fresh water.


[See my follow-up post on Synthetic Genomics and Synthetic Biology.]

Breakthrough Bacteria with 100% Artificial Genes -- Another Coup For Craig Venter

At left is a photo of bacterial cells that have completely synthetic DNA. It is not a "synthetic cell" because they actually transplanted the artificial genes into a natural cell. That is, the technology to reproduce the rest of the cell's organs does not exist yet -- but we can synthesize the DNA, and the DNA can direct the synthesis of a daughter organisms.  Details are in Science.

The new organism is a synthetic version of  mycoplasma mycoides, which oddly is a parasite of goats and cows. The natural cell host was a closely related organism, mycoplasma capricolum, which causes pneumonia in goats. It seems these are quite small genomes, and that makes the task easier. 


Fans of Depth of Processing may remember my three previous posts on synthetic biology which mention Craig Venter and his institute. Venter sprang to prominence when he sequenced his own personal DNA with private funding at about the same time as the giant multi-national public effort finished. More recently he has made genetically engineered organisms for algae based power.  Venter has been waging a legal battle to get a patent on a synthetic organism, and anti-technology groups have been opposing him. 


The organism is dubbed "Synthia" and Venter's company Synthetic Genomics business plan focusses on what it is not. It does not contain scores of genes deemed non-essential. The hope is that new genes can be simply added to make the organism more useful industrially, pharmacologically or in energy production. This contrast with the conventional genetic engineering approach of putting new genes in a version of e coli. How much better a completely synthetic genome is, will be seen. If it actually permits a simpler more efficient organism, then it will be worth it.  The main feat in Venter's accomplishment was synthesizing so many base pairs without an error that disabled the organism. 


I view this development optimistically, and think what a great time to be alive and see this happening. I have little sympathy for those who think the synthetic biology is the source of some new flavor of evil. 


<<Oscillator Blog for another view>>

Synthetic Organisms and Synthetic Biology

In my post about Exxon's investment in algae-based biofuel, I touched on Synthetic Genomics, a company that promotes Synthetic Biology -- that is making completely de novo (new, from scratch) organisms.

A big player in Synthetic Biology (or SynBio) is the Biobricks Foundation, which is makes DNA kits available for various cellular functions. There is catalog of cellular parts called the "Registry of Standard Biological Parts," which seems like it should be a joke, but its real. The metaphor is clever -- building an organism from Biobricks like building a wall with real bricks.

Aside from the Biobricks people, most of this field seems to be information science people trying build build "wet-ware" and bioethicists toying with interesting up-to-now theoretical issues. The information science types need to harden up and do some molecular biology. Bioethics is fun, but that is not getting the science done either.

Ginkgo Bioworks has a kit for assembling Biobricks. The instructions read like the Bioengineering for Dummies, with pictures and very basic instructions. I wonder if this is directed at hobbyists rather than scientists.

A light-hearted intro to synthetic biology is in this comic from Nature magazine.
The article is from way back in 2005, and it shows the information systems brand of synthetic biology, wherein these new cells are like electronic computers. The comic makes an interesting point about the bioengineers not really understanding what they are doing. (Is that typical of engineers?)

I have not seen any convincing accounts of real synthetic organisms to this point.